Search results for "Tree"

2006

Understanding evolutionary processes that drive genome reduction requires determining the tempo (rate) and the mode (size and types of deletions) of gene losses. In this study, we analysed five endosymbiotic genome sequences of the gamma-proteobacteria (three different Buchnera aphidicola strains, Wigglesworthia glossinidia, Blochmannia floridanus) to test if gene loss could be driven by the selective importance of genes. We used a parsimony method to reconstruct a minimal ancestral genome of insect endosymbionts and quantified gene loss along the branches of the phylogenetic tree. To evaluate the selective or functional importance of genes, we used a parameter that measures the level of ad…

Characterization of two globin genes from the malaria mosquito Anopheles gambiae: Divergent origin of nematoceran haemoglobins

2007

The chironomid midges are the only insects that harbour true haemoglobin in their haemolymph. Here we report the identification of haemoglobin genes in two other nematoceran species. Two paralogous haemoglobin genes (glob1 and glob2) from the malaria mosquito Anopheles gambiae were cloned and sequenced. Furthermore, we identified two orthologous haemoglobin genes in the yellow fever mosquito Aedes aegypti. All four haemoglobins were predicted to be intracellular proteins, with the amino acids required for heme- and oxygen-binding being conserved. In situ-hybridization studies showed that glob1 and glob2 expression in An. gambiae is mainly associated with the tracheal system. This pattern re…

A classification scheme for mobilization regions of bacterial plasmids

2003

Transmissible plasmids can be classified according to their mobilization ability, as being conjugative (self-transmissible) or mobilizable (transmissible only in the presence of additional conjugative functions). Naturally occurring mobilizable plasmids carry the genetic information necessary for relaxosome formation and processing, but lack the functions required for mating pair formation. Mobilizable plasmids have a tremendous impact in horizontal gene transfer in nature, including the spread of antibiotic resistance. However, analysis of their promiscuity and diversity has attracted less attention than that of conjugative plasmids. This review will focus on the analysis of the diversity …

Why Nuclear Ribosomal DNA Spacers (ITS) Tell Different Stories in Quercus

2001

The molecular systematics of Quercus (Fagaceae) was recently assessed by two teams using independently generated ITS sequences. Although the results disagreed in several remarkable features, the phylogenetic trees for either hypothesis were highly supported by bootstrap resampling. We have reanalyzed the ITS sequences used by both teams (eight taxa) to reveal the underlying patterns of this divergence. Within species, conspicuous length and G + C% divergence were evident in most sequence comparisons. In addition, a high rate of substitutions and deletions involving highly conserved motifs in both ITS spacers were present in a set of sequences. This was coupled with a less thermodynamic stab…

Molecular Structure of a Gypsy Element of Drosophila Subobscura (Gypsyds) Constituting a Degenerate Form of Insect Retroviruses

1996

We have determined the nucleotide sequence of a 7.5 kb full-size gypsy element from Drosophila subobscura strain H-271. Comparative analyses were carried out on the sequence and molecular structure of gypsy elements of D.subobscura (gypsyDs), D.melanogaster (gypsyDm) and D.virilis (gypsyDv). The three elements show a structure that maintains a common mechanism of expression. ORF1 and ORF2 show typical motifs of gag and pol genes respectively in the three gypsy elements and could encode functional proteins necessary for intracellular expansion. In the three ORF1 proteins an arginine-rich region was found which could constitute a RNA binding motif. The main differences among the gypsy element…

Partial Sequence Homogenization in the 5S Multigene Families May Generate Sequence Chimeras and Spurious Results in Phylogenetic Reconstructions

2014

Multigene families have provided opportunities for evolutionary biologists to assess molecular evolution processes and phylogenetic reconstructions at deep and shallow systematic levels. However, the use of these markers is not free of technical and analytical challenges. Many evolutionary studies that used the nuclear 5S rDNA gene family rarely used contiguous 5S coding sequences due to the routine use of head-to-tail polymerase chain reaction primers that are anchored to the coding region. Moreover, the 5S coding sequences have been concatenated with independent, adjacent gene units in many studies, creating simulated chimeric genes as the raw data for evolutionary analysis. This practice…

Short duplication in a cDNA clone of the rbcL gene from Picea abies.

1995

The plastidic rbcL gene encodes the LSU of Rubisco (EC 4.1.1.39), the enzyme that catalyzes CO, fixation during photosynthesis (Hallick and Bottomley, 1983). In higher plants the enzyme structure is commonly given as a hexadecameric structure composed of eight LSUs and eight small subunits. Nucleotide sequence data from the rbcL gene have been used extensively in studies of plant phylogeny and molecular evolution (Morden and Golden, 1991; Pasternak and Glick, 1992). To investigate the expression of the rbcL gene in damaged and undamaged Norway spruce trees (Picea abies), we have isolated a rbcL cDNA clone via reverse transcriptasePCR (Table I). Using the proofreading ability of the DNA poly…

rDNA Sequences of <I>Anopheles</I> Species from the Iberian Peninsula and an Evaluation of the 18S rRNA Gene as Phylogenetic Marker in An…

2006

The complete 18S rDNA and internal transcribed spacer (ITS)-2 rDNA sequences were obtained from Anopheles atroparvus Van Thiel and Anopheles plumbeus Stephens from two areas of Spain. The number of nucleotide differences in the 18S rDNA of the two species is high compared with differences in the same gene of other invertebrate vectors. In Anopheles, short 18S rDNA sequences are richer in AT than the longer sequences, which are richer in GC and include extremely GC-biased expanded regions. Four small regions in the variable regions V4 and V7 contain the majority of nucleotide differences. The results did not support the use of partial sequences for relationship analyses. Genetic distances an…

Amplified fragment length polymorphisms and sequence data in the phylogenetic analysis of polyploids: multiple origins of Veronica cymbalaria (Planta…

2007

Summary • The origin of polyploid Veronica cymbalaria (Plantaginaceae) was investigated using DNA sequence data and amplified fragment length polymorphism (AFLP) fingerprints to reveal the parentage of this taxon. The use of AFLP fingerprints in phylogenetic analysis is problematic and various methods have therefore been compared. • DNA sequence data (for the internal transcribed spacer (ITS) region and the plastid trnL-F region (trnL intron, 3’exon, and trnL-F spacer)) and polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) analysis of the ITS region suggested a reliable hypothesis for the evolution of the V. cymbalaria complex. This hypothesis allowed evaluation …

Phylogenetic relationships within the family Halomonadaceae based on comparative 23S and 16S rRNA gene sequence analysis.

2010

A phylogenetic study of the family Halomonadaceae was carried out based on complete 16S rRNA and 23S rRNA gene sequences. Several 16S rRNA genes of type strains were resequenced, and 28 new sequences of the 23S rRNA gene were obtained. Currently, the family includes nine genera (Carnimonas, Chromohalobacter, Cobetia, Halomonas, Halotalea, Kushneria, Modicisalibacter, Salinicola and Zymobacter). These genera are phylogenetically coherent except Halomonas, which is polyphyletic. This genus comprises two clearly distinguished clusters: group 1 includes Halomonas elongata (the type species) and the species Halomonas eurihalina, H. caseinilytica, H. halmophila, H. sabkhae, H. almeriensis, H. hal…